network plot problem
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network plot problem
 
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**Hi,
I wanted to create a network of drugs that are being studied together. So, I created a file as a graph. But plot of my network is not corect! It looks like to me that something else is lying behind this network links created. Could someone help me with this? Thanx! a<-read.graph(file=file.choose(), format="edgelist") plot.igraph(a) File (number present ID of drug): 15 2 10 4 10 4 10 4 13 4 13 4 15 4 18 4 11 5 2 6 7 6 7 6 7 6 12 6 15 6 15 6 19 6 22 6 24 6 6 7 5 12 5 12 7 12 11 12 13 12 13 12 13 12 13 12 16 12 17 12 23 12 23 12 23 12 23 12 6 13 12 13 6 14 6 15 9 15 12 15 13 15 17 16 16 17 1 18 12 18 23 18 2 19 6 19 24 19 21 22 3 25 5 26 6 27 7 27 15 29 20 30 25 31 28 31 8 32 6 33 14 33 22 34 -- ************************** Vlatka Matkovic Puljic +32/ 485/ 453340 [[alternative HTML version deleted]] ______________________________________________ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. |
Re: network plot problem
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Hello,
I don't see the problem. given <- scan(text=" 15 2 10 4 10 4 10 4 13 4 13 4 15 4 18 4 11 5 2 6 7 6 7 6 7 6 12 6 15 6 15 6 19 6 22 6 24 6 6 7 5 12 5 12 7 12 11 12 13 12 13 12 13 12 13 12 16 12 17 12 23 12 23 12 23 12 23 12 6 13 12 13 6 14 6 15 9 15 12 15 13 15 17 16 16 17 1 18 12 18 23 18 2 19 6 19 24 19 21 22 3 25 5 26 6 27 7 27 15 29 20 30 25 31 28 31 8 32 6 33 14 33 22 34 ") mat <- matrix(given, ncol=2, byrow=TRUE) g <- graph(given) # Or, not run (note the transpose) #g <- graph(t(mat)) # The edges are exactly what is given E(g) V(g)$label <- V(g) g$layout <- layout.fruchterman.reingold plot(g, edge.arrow.size=0.5, edge.loop.angle=1, edge.curved=FALSE) So my guess is you've messed up the graph creation. Also, don't post datasets like that, use dput(), lik this: dput(given) c(15, 2, 10, 4, 10, 4, 10, 4, 13, 4, 13, 4, 15, 4, 18, 4, 11, 5, 2, 6, 7, 6, 7, 6, 7, 6, 12, 6, 15, 6, 15, 6, 19, 6, 22, 6, 24, 6, 6, 7, 5, 12, 5, 12, 7, 12, 11, 12, 13, 12, 13, 12, 13, 12, 13, 12, 16, 12, 17, 12, 23, 12, 23, 12, 23, 12, 23, 12, 6, 13, 12, 13, 6, 14, 6, 15, 9, 15, 12, 15, 13, 15, 17, 16, 16, 17, 1, 18, 12, 18, 23, 18, 2, 19, 6, 19, 24, 19, 21, 22, 3, 25, 5, 26, 6, 27, 7, 27, 15, 29, 20, 30, 25, 31, 28, 31, 8, 32, 6, 33, 14, 33, 22, 34) Now all anyone has to do is to copy that output and paste it into an R session. (Try it with the matrix to see the result) Hope this helps, Rui Barradas Em 25-07-2012 16:27, Vlatka Matkovic Puljic escreveu: > **Hi, > > I wanted to create a network of drugs that are being studied together. > So, I created a file as a graph. > But plot of my network is not corect! > It looks like to me that something else is lying behind this network links > created. > > Could someone help me with this? > > Thanx! > > a<-read.graph(file=file.choose(), format="edgelist") > plot.igraph(a) > > File (number present ID of drug): > > 15 2 > 10 4 > 10 4 > 10 4 > 13 4 > 13 4 > 15 4 > 18 4 > 11 5 > 2 6 > 7 6 > 7 6 > 7 6 > 12 6 > 15 6 > 15 6 > 19 6 > 22 6 > 24 6 > 6 7 > 5 12 > 5 12 > 7 12 > 11 12 > 13 12 > 13 12 > 13 12 > 13 12 > 16 12 > 17 12 > 23 12 > 23 12 > 23 12 > 23 12 > 6 13 > 12 13 > 6 14 > 6 15 > 9 15 > 12 15 > 13 15 > 17 16 > 16 17 > 1 18 > 12 18 > 23 18 > 2 19 > 6 19 > 24 19 > 21 22 > 3 25 > 5 26 > 6 27 > 7 27 > 15 29 > 20 30 > 25 31 > 28 31 > 8 32 > 6 33 > 14 33 > 22 34 > > ______________________________________________ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. |
Re: network plot problem
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Thank you Rui.
With matrix works better. I got plot I have expected to have. I want to be undirected. But directed = FALSE or as.undirected(graph) are not working? Where I'd gone wrong? Shouldn't it be possible to add names instead of numbers of nods with vertex.label= ? 2012/7/26 Rui Barradas <[hidden email]> > Hello, > > I don't see the problem. > > given <- scan(text=" > > 15 2 > 10 4 > 10 4 > 10 4 > 13 4 > 13 4 > 15 4 > 18 4 > 11 5 > 2 6 > 7 6 > 7 6 > 7 6 > 12 6 > 15 6 > 15 6 > 19 6 > 22 6 > 24 6 > 6 7 > 5 12 > 5 12 > 7 12 > 11 12 > 13 12 > 13 12 > 13 12 > 13 12 > 16 12 > 17 12 > 23 12 > 23 12 > 23 12 > 23 12 > 6 13 > 12 13 > 6 14 > 6 15 > 9 15 > 12 15 > 13 15 > 17 16 > 16 17 > 1 18 > 12 18 > 23 18 > 2 19 > 6 19 > 24 19 > 21 22 > 3 25 > 5 26 > 6 27 > 7 27 > 15 29 > 20 30 > 25 31 > 28 31 > 8 32 > 6 33 > 14 33 > 22 34 > ") > mat <- matrix(given, ncol=2, byrow=TRUE) > > g <- graph(given) > # Or, not run (note the transpose) > #g <- graph(t(mat)) > # The edges are exactly what is given > E(g) > > V(g)$label <- V(g) > g$layout <- layout.fruchterman.reingold > plot(g, edge.arrow.size=0.5, edge.loop.angle=1, edge.curved=FALSE) > > > So my guess is you've messed up the graph creation. > Also, don't post datasets like that, use dput(), lik this: > > dput(given) > c(15, 2, 10, 4, 10, 4, 10, 4, 13, 4, 13, 4, 15, 4, 18, 4, 11, > 5, 2, 6, 7, 6, 7, 6, 7, 6, 12, 6, 15, 6, 15, 6, 19, 6, 22, 6, > 24, 6, 6, 7, 5, 12, 5, 12, 7, 12, 11, 12, 13, 12, 13, 12, 13, > 12, 13, 12, 16, 12, 17, 12, 23, 12, 23, 12, 23, 12, 23, 12, 6, > 13, 12, 13, 6, 14, 6, 15, 9, 15, 12, 15, 13, 15, 17, 16, 16, > 17, 1, 18, 12, 18, 23, 18, 2, 19, 6, 19, 24, 19, 21, 22, 3, 25, > 5, 26, 6, 27, 7, 27, 15, 29, 20, 30, 25, 31, 28, 31, 8, 32, 6, > 33, 14, 33, 22, 34) > > Now all anyone has to do is to copy that output and paste it into an R > session. > (Try it with the matrix to see the result) > > Hope this helps, > > Rui Barradas > Em 25-07-2012 16:27, Vlatka Matkovic Puljic escreveu: > >> **Hi, >> >> >> I wanted to create a network of drugs that are being studied together. >> So, I created a file as a graph. >> But plot of my network is not corect! >> It looks like to me that something else is lying behind this network links >> created. >> >> Could someone help me with this? >> >> Thanx! >> >> a<-read.graph(file=file.**choose(), format="edgelist") >> plot.igraph(a) >> >> File (number present ID of drug): >> >> 15 2 >> 10 4 >> 10 4 >> 10 4 >> 13 4 >> 13 4 >> 15 4 >> 18 4 >> 11 5 >> 2 6 >> 7 6 >> 7 6 >> 7 6 >> 12 6 >> 15 6 >> 15 6 >> 19 6 >> 22 6 >> 24 6 >> 6 7 >> 5 12 >> 5 12 >> 7 12 >> 11 12 >> 13 12 >> 13 12 >> 13 12 >> 13 12 >> 16 12 >> 17 12 >> 23 12 >> 23 12 >> 23 12 >> 23 12 >> 6 13 >> 12 13 >> 6 14 >> 6 15 >> 9 15 >> 12 15 >> 13 15 >> 17 16 >> 16 17 >> 1 18 >> 12 18 >> 23 18 >> 2 19 >> 6 19 >> 24 19 >> 21 22 >> 3 25 >> 5 26 >> 6 27 >> 7 27 >> 15 29 >> 20 30 >> 25 31 >> 28 31 >> 8 32 >> 6 33 >> 14 33 >> 22 34 >> >> >> > -- ************************** Vlatka Matkovic Puljic gsm: +32.474.894953 [[alternative HTML version deleted]] ______________________________________________ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. |
Re: network plot problem
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Hello,
As for the directed = FALSE, it works with me: g <- graph(given, directed = FALSE) As for the label, it's easy. Create an attribute 'name' and then set the label to that attribute. For instance, using the alphabet's letters, first uppercase. V(g)$name <- c(LETTERS, letters)[V(g)] # or any other names V(g)$label <- V(g)$name Keep 'name' and 'label' separate, like this you may change the label if needed but the name will still be there. Then the plot functions recognise the label attribute. Hope this helps, Rui Barradas Em 27-07-2012 11:37, Vlatka Matkovic Puljic escreveu: > Thank you Rui. > > With matrix works better. I got plot I have expected to have. > > I want to be undirected. But > > directed = FALSE > or > as.undirected(graph) > > are not working? Where I'd gone wrong? > > Shouldn't it be possible to add names instead of numbers of nods with > vertex.label= ? > > > > 2012/7/26 Rui Barradas <[hidden email]> > >> Hello, >> >> I don't see the problem. >> >> given <- scan(text=" >> >> 15 2 >> 10 4 >> 10 4 >> 10 4 >> 13 4 >> 13 4 >> 15 4 >> 18 4 >> 11 5 >> 2 6 >> 7 6 >> 7 6 >> 7 6 >> 12 6 >> 15 6 >> 15 6 >> 19 6 >> 22 6 >> 24 6 >> 6 7 >> 5 12 >> 5 12 >> 7 12 >> 11 12 >> 13 12 >> 13 12 >> 13 12 >> 13 12 >> 16 12 >> 17 12 >> 23 12 >> 23 12 >> 23 12 >> 23 12 >> 6 13 >> 12 13 >> 6 14 >> 6 15 >> 9 15 >> 12 15 >> 13 15 >> 17 16 >> 16 17 >> 1 18 >> 12 18 >> 23 18 >> 2 19 >> 6 19 >> 24 19 >> 21 22 >> 3 25 >> 5 26 >> 6 27 >> 7 27 >> 15 29 >> 20 30 >> 25 31 >> 28 31 >> 8 32 >> 6 33 >> 14 33 >> 22 34 >> ") >> mat <- matrix(given, ncol=2, byrow=TRUE) >> >> g <- graph(given) >> # Or, not run (note the transpose) >> #g <- graph(t(mat)) >> # The edges are exactly what is given >> E(g) >> >> V(g)$label <- V(g) >> g$layout <- layout.fruchterman.reingold >> plot(g, edge.arrow.size=0.5, edge.loop.angle=1, edge.curved=FALSE) >> >> >> So my guess is you've messed up the graph creation. >> Also, don't post datasets like that, use dput(), lik this: >> >> dput(given) >> c(15, 2, 10, 4, 10, 4, 10, 4, 13, 4, 13, 4, 15, 4, 18, 4, 11, >> 5, 2, 6, 7, 6, 7, 6, 7, 6, 12, 6, 15, 6, 15, 6, 19, 6, 22, 6, >> 24, 6, 6, 7, 5, 12, 5, 12, 7, 12, 11, 12, 13, 12, 13, 12, 13, >> 12, 13, 12, 16, 12, 17, 12, 23, 12, 23, 12, 23, 12, 23, 12, 6, >> 13, 12, 13, 6, 14, 6, 15, 9, 15, 12, 15, 13, 15, 17, 16, 16, >> 17, 1, 18, 12, 18, 23, 18, 2, 19, 6, 19, 24, 19, 21, 22, 3, 25, >> 5, 26, 6, 27, 7, 27, 15, 29, 20, 30, 25, 31, 28, 31, 8, 32, 6, >> 33, 14, 33, 22, 34) >> >> Now all anyone has to do is to copy that output and paste it into an R >> session. >> (Try it with the matrix to see the result) >> >> Hope this helps, >> >> Rui Barradas >> Em 25-07-2012 16:27, Vlatka Matkovic Puljic escreveu: >> >>> **Hi, >>> >>> >>> I wanted to create a network of drugs that are being studied together. >>> So, I created a file as a graph. >>> But plot of my network is not corect! >>> It looks like to me that something else is lying behind this network links >>> created. >>> >>> Could someone help me with this? >>> >>> Thanx! >>> >>> a<-read.graph(file=file.**choose(), format="edgelist") >>> plot.igraph(a) >>> >>> File (number present ID of drug): >>> >>> 15 2 >>> 10 4 >>> 10 4 >>> 10 4 >>> 13 4 >>> 13 4 >>> 15 4 >>> 18 4 >>> 11 5 >>> 2 6 >>> 7 6 >>> 7 6 >>> 7 6 >>> 12 6 >>> 15 6 >>> 15 6 >>> 19 6 >>> 22 6 >>> 24 6 >>> 6 7 >>> 5 12 >>> 5 12 >>> 7 12 >>> 11 12 >>> 13 12 >>> 13 12 >>> 13 12 >>> 13 12 >>> 16 12 >>> 17 12 >>> 23 12 >>> 23 12 >>> 23 12 >>> 23 12 >>> 6 13 >>> 12 13 >>> 6 14 >>> 6 15 >>> 9 15 >>> 12 15 >>> 13 15 >>> 17 16 >>> 16 17 >>> 1 18 >>> 12 18 >>> 23 18 >>> 2 19 >>> 6 19 >>> 24 19 >>> 21 22 >>> 3 25 >>> 5 26 >>> 6 27 >>> 7 27 >>> 15 29 >>> 20 30 >>> 25 31 >>> 28 31 >>> 8 32 >>> 6 33 >>> 14 33 >>> 22 34 >>> >>> >>> > ______________________________________________ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. |
Re: network plot problem
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Thank you!
It works fine now! :) 2012/7/27 Rui Barradas <[hidden email]> > Hello, > > As for the directed = FALSE, it works with me: > > g <- graph(given, directed = FALSE) > > As for the label, it's easy. Create an attribute 'name' and then set the > label to that attribute. For instance, using the alphabet's letters, first > uppercase. > > V(g)$name <- c(LETTERS, letters)[V(g)] # or any other names > V(g)$label <- V(g)$name > > Keep 'name' and 'label' separate, like this you may change the label if > needed but the name will still be there. > Then the plot functions recognise the label attribute. > > > Hope this helps, > > Rui Barradas > > Em 27-07-2012 11:37, Vlatka Matkovic Puljic escreveu: > >> Thank you Rui. >> >> With matrix works better. I got plot I have expected to have. >> >> I want to be undirected. But >> >> directed = FALSE >> or >> as.undirected(graph) >> >> are not working? Where I'd gone wrong? >> >> Shouldn't it be possible to add names instead of numbers of nods with >> vertex.label= ? >> >> >> >> 2012/7/26 Rui Barradas <[hidden email]> >> >> Hello, >>> >>> I don't see the problem. >>> >>> given <- scan(text=" >>> >>> 15 2 >>> 10 4 >>> 10 4 >>> 10 4 >>> 13 4 >>> 13 4 >>> 15 4 >>> 18 4 >>> 11 5 >>> 2 6 >>> 7 6 >>> 7 6 >>> 7 6 >>> 12 6 >>> 15 6 >>> 15 6 >>> 19 6 >>> 22 6 >>> 24 6 >>> 6 7 >>> 5 12 >>> 5 12 >>> 7 12 >>> 11 12 >>> 13 12 >>> 13 12 >>> 13 12 >>> 13 12 >>> 16 12 >>> 17 12 >>> 23 12 >>> 23 12 >>> 23 12 >>> 23 12 >>> 6 13 >>> 12 13 >>> 6 14 >>> 6 15 >>> 9 15 >>> 12 15 >>> 13 15 >>> 17 16 >>> 16 17 >>> 1 18 >>> 12 18 >>> 23 18 >>> 2 19 >>> 6 19 >>> 24 19 >>> 21 22 >>> 3 25 >>> 5 26 >>> 6 27 >>> 7 27 >>> 15 29 >>> 20 30 >>> 25 31 >>> 28 31 >>> 8 32 >>> 6 33 >>> 14 33 >>> 22 34 >>> ") >>> mat <- matrix(given, ncol=2, byrow=TRUE) >>> >>> g <- graph(given) >>> # Or, not run (note the transpose) >>> #g <- graph(t(mat)) >>> # The edges are exactly what is given >>> E(g) >>> >>> V(g)$label <- V(g) >>> g$layout <- layout.fruchterman.reingold >>> plot(g, edge.arrow.size=0.5, edge.loop.angle=1, edge.curved=FALSE) >>> >>> >>> So my guess is you've messed up the graph creation. >>> Also, don't post datasets like that, use dput(), lik this: >>> >>> dput(given) >>> c(15, 2, 10, 4, 10, 4, 10, 4, 13, 4, 13, 4, 15, 4, 18, 4, 11, >>> 5, 2, 6, 7, 6, 7, 6, 7, 6, 12, 6, 15, 6, 15, 6, 19, 6, 22, 6, >>> 24, 6, 6, 7, 5, 12, 5, 12, 7, 12, 11, 12, 13, 12, 13, 12, 13, >>> 12, 13, 12, 16, 12, 17, 12, 23, 12, 23, 12, 23, 12, 23, 12, 6, >>> 13, 12, 13, 6, 14, 6, 15, 9, 15, 12, 15, 13, 15, 17, 16, 16, >>> 17, 1, 18, 12, 18, 23, 18, 2, 19, 6, 19, 24, 19, 21, 22, 3, 25, >>> 5, 26, 6, 27, 7, 27, 15, 29, 20, 30, 25, 31, 28, 31, 8, 32, 6, >>> 33, 14, 33, 22, 34) >>> >>> Now all anyone has to do is to copy that output and paste it into an R >>> session. >>> (Try it with the matrix to see the result) >>> >>> Hope this helps, >>> >>> Rui Barradas >>> Em 25-07-2012 16:27, Vlatka Matkovic Puljic escreveu: >>> >>> **Hi, >>>> >>>> >>>> I wanted to create a network of drugs that are being studied together. >>>> So, I created a file as a graph. >>>> But plot of my network is not corect! >>>> It looks like to me that something else is lying behind this network >>>> links >>>> created. >>>> >>>> Could someone help me with this? >>>> >>>> Thanx! >>>> >>>> a<-read.graph(file=file.****choose(), format="edgelist") >>>> >>>> plot.igraph(a) >>>> >>>> File (number present ID of drug): >>>> >>>> 15 2 >>>> 10 4 >>>> 10 4 >>>> 10 4 >>>> 13 4 >>>> 13 4 >>>> 15 4 >>>> 18 4 >>>> 11 5 >>>> 2 6 >>>> 7 6 >>>> 7 6 >>>> 7 6 >>>> 12 6 >>>> 15 6 >>>> 15 6 >>>> 19 6 >>>> 22 6 >>>> 24 6 >>>> 6 7 >>>> 5 12 >>>> 5 12 >>>> 7 12 >>>> 11 12 >>>> 13 12 >>>> 13 12 >>>> 13 12 >>>> 13 12 >>>> 16 12 >>>> 17 12 >>>> 23 12 >>>> 23 12 >>>> 23 12 >>>> 23 12 >>>> 6 13 >>>> 12 13 >>>> 6 14 >>>> 6 15 >>>> 9 15 >>>> 12 15 >>>> 13 15 >>>> 17 16 >>>> 16 17 >>>> 1 18 >>>> 12 18 >>>> 23 18 >>>> 2 19 >>>> 6 19 >>>> 24 19 >>>> 21 22 >>>> 3 25 >>>> 5 26 >>>> 6 27 >>>> 7 27 >>>> 15 29 >>>> 20 30 >>>> 25 31 >>>> 28 31 >>>> 8 32 >>>> 6 33 >>>> 14 33 >>>> 22 34 >>>> >>>> >>>> >>>> >> > -- ************************** Vlatka Matkovic Puljic gsm: +32.474.894953 [[alternative HTML version deleted]] ______________________________________________ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. |
Re: network plot problem
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Is it possible to write a numbers of link next to lines of the network?
For exmple, I have 3 trials that have studied two drugs in network. So, now it seems all links are of same weight. 2012/7/27 Vlatka Matkovic Puljic <[hidden email]> > Thank you! > > It works fine now! :) > > 2012/7/27 Rui Barradas <[hidden email]> > >> Hello, >> >> As for the directed = FALSE, it works with me: >> >> g <- graph(given, directed = FALSE) >> >> As for the label, it's easy. Create an attribute 'name' and then set the >> label to that attribute. For instance, using the alphabet's letters, first >> uppercase. >> >> V(g)$name <- c(LETTERS, letters)[V(g)] # or any other names >> V(g)$label <- V(g)$name >> >> Keep 'name' and 'label' separate, like this you may change the label if >> needed but the name will still be there. >> Then the plot functions recognise the label attribute. >> >> >> Hope this helps, >> >> Rui Barradas >> >> Em 27-07-2012 11:37, Vlatka Matkovic Puljic escreveu: >> >>> Thank you Rui. >>> >>> With matrix works better. I got plot I have expected to have. >>> >>> I want to be undirected. But >>> >>> directed = FALSE >>> or >>> as.undirected(graph) >>> >>> are not working? Where I'd gone wrong? >>> >>> Shouldn't it be possible to add names instead of numbers of nods with >>> vertex.label= ? >>> >>> >>> >>> 2012/7/26 Rui Barradas <[hidden email]> >>> >>> Hello, >>>> >>>> I don't see the problem. >>>> >>>> given <- scan(text=" >>>> >>>> 15 2 >>>> 10 4 >>>> 10 4 >>>> 10 4 >>>> 13 4 >>>> 13 4 >>>> 15 4 >>>> 18 4 >>>> 11 5 >>>> 2 6 >>>> 7 6 >>>> 7 6 >>>> 7 6 >>>> 12 6 >>>> 15 6 >>>> 15 6 >>>> 19 6 >>>> 22 6 >>>> 24 6 >>>> 6 7 >>>> 5 12 >>>> 5 12 >>>> 7 12 >>>> 11 12 >>>> 13 12 >>>> 13 12 >>>> 13 12 >>>> 13 12 >>>> 16 12 >>>> 17 12 >>>> 23 12 >>>> 23 12 >>>> 23 12 >>>> 23 12 >>>> 6 13 >>>> 12 13 >>>> 6 14 >>>> 6 15 >>>> 9 15 >>>> 12 15 >>>> 13 15 >>>> 17 16 >>>> 16 17 >>>> 1 18 >>>> 12 18 >>>> 23 18 >>>> 2 19 >>>> 6 19 >>>> 24 19 >>>> 21 22 >>>> 3 25 >>>> 5 26 >>>> 6 27 >>>> 7 27 >>>> 15 29 >>>> 20 30 >>>> 25 31 >>>> 28 31 >>>> 8 32 >>>> 6 33 >>>> 14 33 >>>> 22 34 >>>> ") >>>> mat <- matrix(given, ncol=2, byrow=TRUE) >>>> >>>> g <- graph(given) >>>> # Or, not run (note the transpose) >>>> #g <- graph(t(mat)) >>>> # The edges are exactly what is given >>>> E(g) >>>> >>>> V(g)$label <- V(g) >>>> g$layout <- layout.fruchterman.reingold >>>> plot(g, edge.arrow.size=0.5, edge.loop.angle=1, edge.curved=FALSE) >>>> >>>> >>>> So my guess is you've messed up the graph creation. >>>> Also, don't post datasets like that, use dput(), lik this: >>>> >>>> dput(given) >>>> c(15, 2, 10, 4, 10, 4, 10, 4, 13, 4, 13, 4, 15, 4, 18, 4, 11, >>>> 5, 2, 6, 7, 6, 7, 6, 7, 6, 12, 6, 15, 6, 15, 6, 19, 6, 22, 6, >>>> 24, 6, 6, 7, 5, 12, 5, 12, 7, 12, 11, 12, 13, 12, 13, 12, 13, >>>> 12, 13, 12, 16, 12, 17, 12, 23, 12, 23, 12, 23, 12, 23, 12, 6, >>>> 13, 12, 13, 6, 14, 6, 15, 9, 15, 12, 15, 13, 15, 17, 16, 16, >>>> 17, 1, 18, 12, 18, 23, 18, 2, 19, 6, 19, 24, 19, 21, 22, 3, 25, >>>> 5, 26, 6, 27, 7, 27, 15, 29, 20, 30, 25, 31, 28, 31, 8, 32, 6, >>>> 33, 14, 33, 22, 34) >>>> >>>> Now all anyone has to do is to copy that output and paste it into an R >>>> session. >>>> (Try it with the matrix to see the result) >>>> >>>> Hope this helps, >>>> >>>> Rui Barradas >>>> Em 25-07-2012 16:27, Vlatka Matkovic Puljic escreveu: >>>> >>>> **Hi, >>>>> >>>>> >>>>> I wanted to create a network of drugs that are being studied together. >>>>> So, I created a file as a graph. >>>>> But plot of my network is not corect! >>>>> It looks like to me that something else is lying behind this network >>>>> links >>>>> created. >>>>> >>>>> Could someone help me with this? >>>>> >>>>> Thanx! >>>>> >>>>> a<-read.graph(file=file.****choose(), format="edgelist") >>>>> >>>>> plot.igraph(a) >>>>> >>>>> File (number present ID of drug): >>>>> >>>>> 15 2 >>>>> 10 4 >>>>> 10 4 >>>>> 10 4 >>>>> 13 4 >>>>> 13 4 >>>>> 15 4 >>>>> 18 4 >>>>> 11 5 >>>>> 2 6 >>>>> 7 6 >>>>> 7 6 >>>>> 7 6 >>>>> 12 6 >>>>> 15 6 >>>>> 15 6 >>>>> 19 6 >>>>> 22 6 >>>>> 24 6 >>>>> 6 7 >>>>> 5 12 >>>>> 5 12 >>>>> 7 12 >>>>> 11 12 >>>>> 13 12 >>>>> 13 12 >>>>> 13 12 >>>>> 13 12 >>>>> 16 12 >>>>> 17 12 >>>>> 23 12 >>>>> 23 12 >>>>> 23 12 >>>>> 23 12 >>>>> 6 13 >>>>> 12 13 >>>>> 6 14 >>>>> 6 15 >>>>> 9 15 >>>>> 12 15 >>>>> 13 15 >>>>> 17 16 >>>>> 16 17 >>>>> 1 18 >>>>> 12 18 >>>>> 23 18 >>>>> 2 19 >>>>> 6 19 >>>>> 24 19 >>>>> 21 22 >>>>> 3 25 >>>>> 5 26 >>>>> 6 27 >>>>> 7 27 >>>>> 15 29 >>>>> 20 30 >>>>> 25 31 >>>>> 28 31 >>>>> 8 32 >>>>> 6 33 >>>>> 14 33 >>>>> 22 34 >>>>> >>>>> >>>>> >>>>> >>> >> > > > -- > ************************** > Vlatka Matkovic Puljic > gsm: +32.474.894953 > > -- ************************** Vlatka Matkovic Puljic gsm: +32.474.894953 [[alternative HTML version deleted]] ______________________________________________ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. |
Re: network plot problem
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Hello,
It's more or less the same it was with vertices. If the edge labels represent weights, then create an appropriate attribute and set the labels' values to that attribute's values: E(g)$weight <- something # keep the weights in a separate attribute E(g)$label <- E(g)$weight # set when needed The plot function now uses these edge labels. Rui Barradas Em 28-07-2012 17:44, Vlatka Matkovic Puljic escreveu: > Is it possible to write a numbers of link next to lines of the network? > > For exmple, I have 3 trials that have studied two drugs in network. > So, now it seems all links are of same weight. > > > > > > 2012/7/27 Vlatka Matkovic Puljic <[hidden email]> > >> Thank you! >> >> It works fine now! :) >> >> 2012/7/27 Rui Barradas <[hidden email]> >> >>> Hello, >>> >>> As for the directed = FALSE, it works with me: >>> >>> g <- graph(given, directed = FALSE) >>> >>> As for the label, it's easy. Create an attribute 'name' and then set the >>> label to that attribute. For instance, using the alphabet's letters, first >>> uppercase. >>> >>> V(g)$name <- c(LETTERS, letters)[V(g)] # or any other names >>> V(g)$label <- V(g)$name >>> >>> Keep 'name' and 'label' separate, like this you may change the label if >>> needed but the name will still be there. >>> Then the plot functions recognise the label attribute. >>> >>> >>> Hope this helps, >>> >>> Rui Barradas >>> >>> Em 27-07-2012 11:37, Vlatka Matkovic Puljic escreveu: >>> >>>> Thank you Rui. >>>> >>>> With matrix works better. I got plot I have expected to have. >>>> >>>> I want to be undirected. But >>>> >>>> directed = FALSE >>>> or >>>> as.undirected(graph) >>>> >>>> are not working? Where I'd gone wrong? >>>> >>>> Shouldn't it be possible to add names instead of numbers of nods with >>>> vertex.label= ? >>>> >>>> >>>> >>>> 2012/7/26 Rui Barradas <[hidden email]> >>>> >>>> Hello, >>>>> I don't see the problem. >>>>> >>>>> given <- scan(text=" >>>>> >>>>> 15 2 >>>>> 10 4 >>>>> 10 4 >>>>> 10 4 >>>>> 13 4 >>>>> 13 4 >>>>> 15 4 >>>>> 18 4 >>>>> 11 5 >>>>> 2 6 >>>>> 7 6 >>>>> 7 6 >>>>> 7 6 >>>>> 12 6 >>>>> 15 6 >>>>> 15 6 >>>>> 19 6 >>>>> 22 6 >>>>> 24 6 >>>>> 6 7 >>>>> 5 12 >>>>> 5 12 >>>>> 7 12 >>>>> 11 12 >>>>> 13 12 >>>>> 13 12 >>>>> 13 12 >>>>> 13 12 >>>>> 16 12 >>>>> 17 12 >>>>> 23 12 >>>>> 23 12 >>>>> 23 12 >>>>> 23 12 >>>>> 6 13 >>>>> 12 13 >>>>> 6 14 >>>>> 6 15 >>>>> 9 15 >>>>> 12 15 >>>>> 13 15 >>>>> 17 16 >>>>> 16 17 >>>>> 1 18 >>>>> 12 18 >>>>> 23 18 >>>>> 2 19 >>>>> 6 19 >>>>> 24 19 >>>>> 21 22 >>>>> 3 25 >>>>> 5 26 >>>>> 6 27 >>>>> 7 27 >>>>> 15 29 >>>>> 20 30 >>>>> 25 31 >>>>> 28 31 >>>>> 8 32 >>>>> 6 33 >>>>> 14 33 >>>>> 22 34 >>>>> ") >>>>> mat <- matrix(given, ncol=2, byrow=TRUE) >>>>> >>>>> g <- graph(given) >>>>> # Or, not run (note the transpose) >>>>> #g <- graph(t(mat)) >>>>> # The edges are exactly what is given >>>>> E(g) >>>>> >>>>> V(g)$label <- V(g) >>>>> g$layout <- layout.fruchterman.reingold >>>>> plot(g, edge.arrow.size=0.5, edge.loop.angle=1, edge.curved=FALSE) >>>>> >>>>> >>>>> So my guess is you've messed up the graph creation. >>>>> Also, don't post datasets like that, use dput(), lik this: >>>>> >>>>> dput(given) >>>>> c(15, 2, 10, 4, 10, 4, 10, 4, 13, 4, 13, 4, 15, 4, 18, 4, 11, >>>>> 5, 2, 6, 7, 6, 7, 6, 7, 6, 12, 6, 15, 6, 15, 6, 19, 6, 22, 6, >>>>> 24, 6, 6, 7, 5, 12, 5, 12, 7, 12, 11, 12, 13, 12, 13, 12, 13, >>>>> 12, 13, 12, 16, 12, 17, 12, 23, 12, 23, 12, 23, 12, 23, 12, 6, >>>>> 13, 12, 13, 6, 14, 6, 15, 9, 15, 12, 15, 13, 15, 17, 16, 16, >>>>> 17, 1, 18, 12, 18, 23, 18, 2, 19, 6, 19, 24, 19, 21, 22, 3, 25, >>>>> 5, 26, 6, 27, 7, 27, 15, 29, 20, 30, 25, 31, 28, 31, 8, 32, 6, >>>>> 33, 14, 33, 22, 34) >>>>> >>>>> Now all anyone has to do is to copy that output and paste it into an R >>>>> session. >>>>> (Try it with the matrix to see the result) >>>>> >>>>> Hope this helps, >>>>> >>>>> Rui Barradas >>>>> Em 25-07-2012 16:27, Vlatka Matkovic Puljic escreveu: >>>>> >>>>> **Hi, >>>>>> >>>>>> I wanted to create a network of drugs that are being studied together. >>>>>> So, I created a file as a graph. >>>>>> But plot of my network is not corect! >>>>>> It looks like to me that something else is lying behind this network >>>>>> links >>>>>> created. >>>>>> >>>>>> Could someone help me with this? >>>>>> >>>>>> Thanx! >>>>>> >>>>>> a<-read.graph(file=file.****choose(), format="edgelist") >>>>>> >>>>>> plot.igraph(a) >>>>>> >>>>>> File (number present ID of drug): >>>>>> >>>>>> 15 2 >>>>>> 10 4 >>>>>> 10 4 >>>>>> 10 4 >>>>>> 13 4 >>>>>> 13 4 >>>>>> 15 4 >>>>>> 18 4 >>>>>> 11 5 >>>>>> 2 6 >>>>>> 7 6 >>>>>> 7 6 >>>>>> 7 6 >>>>>> 12 6 >>>>>> 15 6 >>>>>> 15 6 >>>>>> 19 6 >>>>>> 22 6 >>>>>> 24 6 >>>>>> 6 7 >>>>>> 5 12 >>>>>> 5 12 >>>>>> 7 12 >>>>>> 11 12 >>>>>> 13 12 >>>>>> 13 12 >>>>>> 13 12 >>>>>> 13 12 >>>>>> 16 12 >>>>>> 17 12 >>>>>> 23 12 >>>>>> 23 12 >>>>>> 23 12 >>>>>> 23 12 >>>>>> 6 13 >>>>>> 12 13 >>>>>> 6 14 >>>>>> 6 15 >>>>>> 9 15 >>>>>> 12 15 >>>>>> 13 15 >>>>>> 17 16 >>>>>> 16 17 >>>>>> 1 18 >>>>>> 12 18 >>>>>> 23 18 >>>>>> 2 19 >>>>>> 6 19 >>>>>> 24 19 >>>>>> 21 22 >>>>>> 3 25 >>>>>> 5 26 >>>>>> 6 27 >>>>>> 7 27 >>>>>> 15 29 >>>>>> 20 30 >>>>>> 25 31 >>>>>> 28 31 >>>>>> 8 32 >>>>>> 6 33 >>>>>> 14 33 >>>>>> 22 34 >>>>>> >>>>>> >>>>>> >>>>>> >> >> -- >> ************************** >> Vlatka Matkovic Puljic >> gsm: +32.474.894953 >> >> > ______________________________________________ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. |
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